Thank you so much for your thorough and thoughtful reply! I particularly enjoyed the article by Francis Heylighen as he raised an issue in the discussion of complexity in biological systems which I had not yet researched  namely, does evolution increase complexity?

In investigating the subject a bit further, I discovered some things you and the others here might also find quite interesting. Chief among these is that there is a formulation for functional complexity in complex systems which includes biological systems. The evolutionary biologists however seem to question the applicability of the term to their domain and have offered yet another type of complexity, physical complexity. Heylighens article (1996) did not use the term which was evidently coined by Adami. Following is an article by Adami raising the concept and the results of modeling the theory:

Darwinian evolution is a simple yet powerful process that requires only a population of reproducing organisms in which each offspring has the potential for a heritable variation from its parent. This principle governs evolution in the natural world, and has gracefully produced organisms of vast complexity. Still, whether or not complexity increases through evolution has become a contentious issue. Gould (1), for example, argues that any recognizable trend can be explained by the "drunkard's walk" model, where "progress" is due simply to a fixed boundary condition. McShea (2) investigates trends in the evolution of certain types of structural and functional complexity, and finds some evidence of a trend but nothing conclusive. In fact, he concludes that "something may be increasing. But is it complexity?" Bennett (3), on the other hand, resolves the issue by fiat, defining complexity as "that which increases when self-organizing systems organize themselves." Of course, to address this issue, complexity needs to be both defined and measurable.

In this paper, we skirt the issue of structural and functional complexity by examining genomic complexity. It is tempting to believe that genomic complexity is mirrored in functional complexity and vice versa. Such an hypothesis, however, hinges upon both the aforementioned ambiguous definition of complexity and the obvious difficulty of matching genes with function. Several developments allow us to bring a new perspective to this old problem. On the one hand, genomic complexity can be defined in a consistent information-theoretic manner [the "physical" complexity (4)], which appears to encompass intuitive notions of complexity used in the analysis of genomic structure and organization (5). On the other hand, it has been shown that evolution can be observed in an artificial medium (6, 7), providing a unique glimpse at universal aspects of the evolutionary process in a computational world. In this system, the symbolic sequences subject to evolution are computer programs that have the ability to self-replicate via the execution of their own code. In this respect, they are computational analogs of catalytically active RNA sequences that serve as the templates of their own reproduction. In populations of such sequences that adapt to their world (inside of a computer's memory), noisy self-replication coupled with finite resources and an information-rich environment leads to a growth in sequence length as the digital organisms incorporate more and more information about their environment into their genome. Evolution in an information-poor landscape, on the contrary, leads to selection for replication only, and a shrinking genome size as in the experiments of Spiegelman and colleagues (8). These populations allow us to observe the growth of physical complexity explicitly, and also to distinguish distinct evolutionary pressures acting on the genome and analyze them in a mathematical framework.

If an organism's complexity is a reflection of the physical complexity of its genome (as we assume here), the latter is of prime importance in evolutionary theory. Physical complexity, roughly speaking, reflects the number of base pairs in a sequence that are functional. As is well known, equating genomic complexity with genome length in base pairs gives rise to a conundrum (known as the C-value paradox) because large variations in genomic complexity (in particular in eukaryotes) seem to bear little relation to the differences in organismic complexity (9). The C-value paradox is partly resolved by recognizing that not all of DNA is functional: that there is a neutral fraction that can vary from species to species. If we were able to monitor the non-neutral fraction, it is likely that a significant increase in this fraction could be observed throughout at least the early course of evolution. For the later period, in particular the later Phanerozoic Era, it is unlikely that the growth in complexity of genomes is due solely to innovations in which genes with novel functions arise de novo. Indeed, most of the enzyme activity classes in mammals, for example, are already present in prokaryotes (10). Rather, gene duplication events leading to repetitive DNA and subsequent diversification (11) as well as the evolution of gene regulation patterns appears to be a more likely scenario for this stage. Still, we believe that the Maxwell Demon mechanism described below is at work during all phases of evolution and provides the driving force toward ever increasing complexity in the natural world.

Conclusions: The physical complexity of those regions that do not code for the structural changes increases independently from structural complexity. There is no correlation between fitness of collectives and division of labor (possible causes will be discussed later). On the other hand, there is a correlation between the size of colonies and fitness. Thus, it seems that there is no additional increase of physical complexity other than those regions that code for structural changes

Seems to me that result ought to renew our interest in what is functional complexity with regard to biological systems. Here is the definition from the complex systems corner:

Complexity is ...[the abstract notion of complexity has been captured in many different ways. Most, if not all of these, are related to each other and they fall into two classes of definitions]:

1) ...the (minimal) length of a description of the system.

2) ...the (minimal) amount of time it takes to create the system.

The length of a description is measured in units of information. The former definition is closely related to Shannon information theory and algorithmic complexity, and the latter is related to computational complexity.

1) ...what parts of a system do together that they would not do by themselves: collective behavior.

2) ...what a system does by virtue of its relationship to its environment that it would not do by itself: e.g. its function.

3) ...the act or process of becoming an emergent system.

According to (1) emergence refers to understanding how collective properties arise from the properties of parts. More generally, it refers to how behavior at a larger scale of the system arises from the detailed structure, behavior and relationships on a finer scale. In the extreme, it is about how macroscopic behavior arises from microscopic behavior.

According to this view, when we think about emergence we are, in our mind's eye, moving between different vantage points. We see the trees and the forest at the same time. We see the way the trees and the forest are related to each other. To see in both these views we have to be able to see details, but also ignore details. The trick is to know which of the many details we see in the trees are important to know when we see the forest.

In conventional views the observer considers either the trees or the forest. Those who consider the trees consider the details to be essential and do not see the patterns that arise when considering trees in the context of the forest. Those who consider the forest do not see the details. When one can shift back and forth between seeing the trees and the forest one also sees which aspects of the trees are relevant to the description of the forest. Understanding this relationship in general is the study of emergence.

Given a system whose function we want to specify, for which the environmental (input) variables have a complexity of C(e), and the actions of the system have a complexity of C(a), then the complexity of specification of the function of the system is:

C(f)=C(a) 2 C(e)

Where complexity is defined as the logarithm (base 2) of the number of possibilities or, equivalently, the length of a description in bits. The proof follows from recognizing that a complete specification of the function is given by a table whose rows are the actions (C(a) bits) for each possible input, of which there are 2 C(e). Since no restriction has been assumed on the actions, all actions are possible and this is the minimal length description of the function. Note that this theorem applies to the complexity of description as defined by the observer, so that each of the quantities can be defined by the desires of the observer for descriptive accuracy. This theorem is known in the study of Boolean functions (binary functions of binary variables) but is not widely understood as a basic theorem in complex systems[15]. The implications of this theorem are widespread and significant to science and engineering.

IMHO, the science of complex systems - function, observer and emergence  would have accomplished the same distinction that Michael Behe targeted with his new term, irreducible complexity. By introducing a new term under color of Intelligent Design, it gave the concept a taint of ideology. Compare the above definitions to the definition of irreducible complexity:

"a single system which is composed of several interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning" (Michael Behe, Molecular Machines: Experimental Support for the Design Inference)

Believers in the intelligent design theory use this term to refer to biological systems and organs that could not have come about by a series of small changes. For such mechanisms or organs, anything less than their complete form would not work at all, or would in fact be a detriment to the organism, and would therefore never survive the process of natural selection. Proponents of intelligent design argue that while some complex systems and organs can be explained by evolution, organs and biological features which are irreducibly complex cannot be explained by current models, and that an intelligent designer must thus have created or guided life.

You continued with a few other comments:

Von Neumann has presented a scientific challenge evolutionary theorists have yet to address fully. But I believe that the field of Biosemotics -- the quote I put up from Rocha above falls within this category -- is answering his challenge, though the discipline is still in its infancy and the response is not yet adequate to be qualified as an answer.

I certainly agree that the field is not fully developed wrt biology (though much progress has been made in the mathematics by Wolfram et al). Personally, I believe the evolutionary theorists will be brought kicking and screaming to the theory simply because the theory goes to complex systems arising from the iteration of simple rules. That would speak against happenstance and for direction. For Lurkers interested in the subject:

The key to understanding all the dialogue on the Chowder Society is communications. In ordinary conversation  and indeed, in many of the articles from the science community at large  information and message are treated as pretty much the same thing. A database, letter, diagram, DNA would all be considered information using various symbolizations or languages for comprehension.

But to understand the Shannon definition, one must view information as a reduction of uncertainty in a receiver  the communication itself having been successfully completed. In molecular machines this is vital and can be best visualized by comparing a dead skin cell to a live one. The DNA, or message, is as good dead as alive. But the live skin cell successfully communicates with itself and the environment.

The state changes that occur in the molecular machinery is evidence of the reduction of uncertainty in the receiver. This is akin to the state changes which Rocha indicates would be required in an RNA world (abiogenesis) for self-organizing complexity to begin  i.e. toggling between autonomous communication and communication with the environment.

And "randomness" taken by itself is meaningless unless it is specifically applied to a scientific formulation of a theory that can be tested. Mathematicians have raised problems with "randomness" in general, some evolutionary theorists are dealing with it as it applies to natural selection, but we cannot use it as an alternative to either explanations for the origin of life on earth or problems within evolutionary theory unless it is attached to a specific theory whose applicability can be tested.

I agree that randomness is problematic from the get-go. It is a problem for the theory of evolution as it was originally formulated, thats why I suggest the theory needs to be brought up-to-date. It is a big problem for abiogenesis, too  because logically there must be some break point population from which the theoretical RNA world could be bootstrapped into replication. IOW, it would require much more than a single phenomenon in a vast population of opportunity.

One way or another we are going to have to see something offered by Intelligent Design theorists or supporters of the theory, that attempts to make an argument based upon evidence, something like "result x has likely occured because of evidence y occuring at time z." It is not enough to simply challenge the body of scientific study to the contrary in an attempt to negate its hypotheses and/or conclusions and, as a result, leave Intelligent Design theory as the only possible alternative. That is not scientific under any criteria that are worthy of being considered as falling within "science."

IMHO, the Intelligent Design fellows at Discovery Institute are essentially minor players wrt the subject of happenstance in biological systems. They are much resented because of an assumed theological agenda  the same objection many of us have against the metaphysical naturalists like Lewontin who promote atheism under the color of science.

To the contrary, IMHO, the whole notion of happenstance is dying with a whimper because of the work of general mathematicians, information theorists and physicists. Precious few of them have a perceptible metaphysical bias, but they keep coming back to theories which make an unintended theological statement, that biological systems did not arise by happenstance alone. This is much like the determination that there was a beginning  the most theological statement to come out of science.

That was a very thorough and well-formatted reply Alamo-Girl. Though I am getting even farther behind in that I still owe betty a response on the "Plato" thread, I must defer to a later time when I can address what you have raised in a more comprehensive manner. Given the completeness of your post I think it would be untoward of me to simply dismiss what you have written, and I won't do that even when I do respond because some of what you have stated I agree with, so I will ask your indulgence to wait until I have a little more free time on my hands before I reply. I'm just stopping by right now during a work break and I am entering a busy week in which I have to complete some daunting job tasks that are going to occupy a good deal of my time, some of which will likely run beyond regular working hours.

I'll be back later, though I cannot say just when, though I'll try to get in here tonight. I owe betty a response first.

Thank you so much for your reply! I do very much understand the need to take care of pressing deadlines, so please, by all means, take your time in responding to both betty boop and to me. We will patiently look forward to your posts!

Thank you so much for that link! It was a fascinating read. Evidently, Rothschild was the first to coin the term "biosemiotics" and he obviously was addressing spiritual aspects as well as the biological aspects.

Biosemiotics (bios=life & semion=sign) is a growing field that studies the production, action and interpretation of signs in the physical and biologic realm, in an attempt to integrate the findings of scientific biology and semiotics to form a new view of life and meaning as immanent features of the natural world. The term "biosemiotic" was first used by F.S.Rothschild in 1962, but Thomas Sebeok has done much to popularize the term and field.

Thus, biosemiotics is

biology interpreted as sign systems

or, to use a few more words,

the signification, communication and habit formation of living processes

semiosis (changing sign relations) in living nature

the biological basis of all signs and sign interpretation

To define biosemiotics as biology interpreted as sign systems is to emphasize not only the close relation between biology as we know it (as a scientific field of inquiry) and semiotics (the study of signs), but primarily the profound change of perspective implied when life is considered not just from the perspectives of molecules and chemistry, but as signs conveyed and interpreted by other living signs in a variety of ways, including by means of molecules. In this sense, biosemiotics takes for granted and respects the complexity of living processes as revealed by the existing fields of biology - from molecular biology to brain science and behavioural studies - however, biosemiotics attempts to bring together separate findings of the various disciplines of biology (including evolutionary biology) into a new and more unified perspective on the central phenomena of the living world, including the generation of function and signification in living systems, from the ribosome to the ecosystem and from the beginnings of life to its ultimate meanings.

To sum it up wrt this discussion, biosemiosis is the sign - or symbolization (Pattee, Rocha); it is the language of the message in living systems.

The area of study differs from the approach of applying Claude Shannon's mathematical theory of communication (information theory) to molecular machines in that biosemiosis is focused on the symbolization of the message whereas the later is focused on the successful communication itself.

But when taken up by mathematicians the two directions of inquiry overlap:

I've just posted a reply to betty on the Plato thread and it took me about two hours to compose it, so I'm afraid I've used up my available "Freeper Minutes" for the day. I've got to turn in and get ready for another busy one tomorrow. I still owe you a reply on your earlier post and I'll need some more free time before I can get to it.

IMHO, this review illustrates the reviewers failure to understand the difference between the message and the communication of the message  as he ignores much to reduce the entire process to decoding. Most of his concerns center on his suspicion that Yockey is an intelligent design theorist or creationist.

On the handy side though, the webpage includes a graphic which illustrates and compares the Shannon communication model in normal engineering v biological systems (though he ignores both the communication and the rise of symbolization in his review).

Yockey responded to the above review in an email dated Nov 13, 2000:

Dear Gert:

Thank for your review of my book Information Theory and Molecular Biology. This book is now out of print but I am working on the second edition.

You seem puzzled by my quotations of the Bible. Please note that I also quote Robert Frost, Homer's Iliad, the Mikado, Charles Darwin, Machiavelli''s The Prince, Plato, The Rubaiyat and other sources. When something was said 2000 years ago, it is plagiarism to say it again without quotation.

It is a viscous circle indeed! (*) But that is what we find by experiment. We are the product of nature not its judge. As Hamlet said to his friend: "There are many things, Horatio, between Heaven and Earth unknown in your philosophy."

See Gregory Chaitin's books "The Limits of Mathematics",1998 and "The Unknowable",1999 both Springer-Verlag. See also my comments on unknowability in Epilogue. We will never know what caused the Big Bang and we will never know what caused life.

By the way, I am indeed an anti-creationist becaue I believe that the origin of life is, like the Big Bang, a part of nature but is unknowable to man.

Taken all in all, especially for those who finished reading the review, it is very favorable.

Here is a list of my recent publications. If you send me your postal address I shall send you the Computers & Chemistry paper. That will explain why the recent data on the genomes of human and other organisms provide a mathematical proof of "Darwinism" beyond a reasonable doubt. (**) I suggest you read the paper in Perspectives in Biology and Medicine. Perhaps you would then like to read some of Walther Löb's papers. Stanley Miller was not the first to find amino acids in the silent electrical discharge.

If someone says that information = uncertainty = entropy, then they are confused, or something was not stated that should have been. Those equalities lead to a contradiction, since entropy of a system increases as the system becomes more disordered. So information corresponds to disorder according to this confusion.

If you always take information to be a decrease in uncertainty at the receiver and you will get straightened out:

and Pi is the probability of the ith symbol. If you don't understand this, please refer to "Is There a Quick Introduction to Information Theory Somewhere?".

Imagine that we are in communication and that we have agreed on an alphabet. Before I send you a bunch of characters, you are uncertain (Hbefore) as to what I'm about to send. After you receive a character, your uncertainty goes down (to Hafter). Hafter is never zero because of noise in the communication system. Your decrease in uncertainty is the information (R) that you gain.

Since Hbefore and Hafter are state functions, this makes R a function of state. It allows you to lose information (it's called forgetting). You can put information into a computer and then remove it in a cycle.

Many of the statements in the early literature assumed a noiseless channel, so the uncertainty after receipt is zero (Hafter=0). This leads to the SPECIAL CASE where R = Hbefore. But Hbefore is NOT "the uncertainty", it is the uncertainty of the receiver BEFORE RECEIVING THE MESSAGE.

The post continues with an example in DNA binding sites.

And here is a message posted by Yockey on the Chowder Society in response to abiogenesis: Yockey #7

To: Brian D. Harper:

I have been lurking in this newsgroup for some time. You have understood my articles and my book. Congratulations. I directed the book to molecular biologists, applied mathematicians and theoretical physicists. It is nice to have someone from Applied Mechanics. Has there been any conversation about this at the faculty club?

"Your book gets discussed here every now and then. I am hoping that people will take this opportunity to pose their questions to the author himself, rather than get second-hand interpretations. I will list below what I feel are some of your more controversial views that should be of interest to this group. Please feel free to modify these if I mis-represent your views in any way ;-)"

You asked three questions:

a) the primeval soup probably never existed

b) even if it did, the various self-organizational schemes proposed to "explain" the origin of life still don't work

c) life must be accepted as an axiom

You get an A!

Response to a) The correct way to pose that statement is: There is no evidence that a primeval soup ever existed. If one looks for geological evidence that a primeval soup existed one comes up empty. See discussion in Information in Bits and Bytes in BioEssays v17 85-88 1995.

There is a more thorough discussion in Information Theory and Molecular Biology. Dialectical materialists are atheists. Their belief in a primeval soup without evidence puts them in bed with theologians. In science the "Absence of evidence IS evidence of absence." One does not believe unless and until one has overwhelming evidence. You will note of course that this is a twist from the usual declaration of faith by SETI disciples. Forgive me if I think this incongruous situation is very funny.

Response to b) All dialectical materialist origin of life scenarios require in extremis a primeval soup. There is no path from this mythical soup to the generation of a genome and a genetic code. John von Neumann showed that fact in his Theory of Self-Reproducing Automata U of Ill. Press 1966. One must begin with a genetic message of a rather large information content. Manfred Eigen and his disciples argue that all it takes is one self-catalytic molecule to generate a genome. This self-catalytic molecule must have a very small information content. By that token, there must be very few of them [Section 2.4.1] As they self-reproduce and evolve the descendants get lost in the enormous number of possible sequences in which the specific messages of biological are buried. From the Shannon-McMillan theorem I have shown that a small protein, cytochrome c is only 2 x 10^-44 of the possible sequences. It takes religious faith to believe that would happen. Of course the minimum information content of the simplest organism is much larger than the information content of cytochrome c.

c) Niels Bohr in his Light and Life [Nature 1933 v131 p421-423; 457-459] lecture is the author of the suggestion that life must be taken as an axiom inasmuch as we take the quantum of action in quantum theory as an axiom. There are many other examples in relativity and quantum mechanics. Prominent among these is the wave-particle dualism. How can an electron, clearly a matter particle, be at once a wave and a particle?

Pose this proposition to your enemies (not your friends): Given any two theories, an experiment will decide between them and prove one true and one false. This is the philosophy of Sir Karl Popper. When a physicist does an experiment to prove that an electron is a particle, it behaves as a particle. When another physicist does an experiment to show an electron is a wave, it behaves as a wave. In some diffraction experiments ray tracing shows the electron or neutron was in two places at once. Thus these experiments prove the wave-particle dualism. Einstein was extremely annoyed by this and suggested experiments to explain what he regarded as a dilemma. He exclaimed: Der lieber Gott wuerfelt nicht mit der Welt! Bohr's reply was: "Einstein, stop telling God what to do!"

Faced with what physicstis and chemists have had to accept from relativity and quantum mechanics, taking the origin of life as an axiom seems rather tame.

In the book I discussed other mathematically deeper questions, for example undecidability. Until the work of Goedel and Turing it was assummed that a mathematical proposition was either true of false. They proved that some questions are undecidable. For example, given any computer program it is undecidable whether it will ever stop. One can check it empirically. But suppose it doesn't stop in one year, no one can be sure it wouldn't stop in another five minutes. So it is with the origin of life.

The dialectical materialist lumpen-intelligentsia are extremely annoyed that God didn't take their advice when He made the universe.

Nonsense. Hydrothermal systems that exhibit complex organic chemistry bootstrapping are known to exist today in some corners of the world.

b) even if it did, the various self-organizational schemes proposed to "explain" the origin of life still don't work

Nonsense. Significant biochemistry substructures are observed to be generated in the systems referenced above. However, the chemistry of this catalytic self-assembly is not fully understood.

c) life must be accepted as an axiom

Nonsense. Life is not even well-defined, and becomes very fuzzy under scrutiny in practice -- there is no such thing as a closed system. Regardless, "life" is an arbitrary categorization based on a set of system properties, not an axiom. (In a sense, this makes the above argument a circular definition.)

151
posted on 12/15/2004 9:53:58 AM PST
by tortoise
(All these moments lost in time, like tears in the rain.)

But, er, you have provided no evidence - source references we can use to explore what you have just said.

I'm particularly interested in evidence of "hydrothermal systems that exhibit complex organic chemistry bootstrapping" - providing of course that the chemistry evidences both autonomy and symbolization in support of successful communication. This is the quandary suggested at the end of Pattee's essay.

Also - if you have anything more up-to-date than Rocha's work with regard to possible mechanisms for the rise of self-organizing complexity in an RNA world, I'd love to read about it!

I do however dispute your conclusion that life is not yet well defined. It seems to me that the comparison between a live skin cell and a dead skin cell makes the point rather well. The live skin cell is communicating successfully (Shannon information theory) with itself and its environment. The DNA and chemistry, OTOH, is as good dead as alive.

I'm terribly sorry for my last post being so flippant. I should never try to post anything while my dog is insisting on a walk.

What I should have done is put my request for source information and the response to the "what is life?" issue in context. Unlike ever so many other evolution related discussions on the forum, this one is seeking to explore the issue of complexity in biological life.

For that reason the overarching information theory (your expertise) is the main entree - hence the out-of-hand response about successful communication (information, Shannon) being peculiar to life. The chemistry is of course also very interesting, especially if we can see how self-organized complexity can be initiated in an RNA world.

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